On Tue, May 3, 2011 at 10:00 AM, Robin Mjelle <robinmje...@gmail.com> wrote:
> Dear User,
>
> I am trying to use the tool "Compute quality statistics" in galaxy on
> Ilumina single reads. The file is 2.3 Gb, fastq format. I have performed
> Quality format converter on the data set and the format is now qualillumina.
> Despite of this, galaxy don't recognize any dataset in the workflow to use
> as input into quality statistics.
> Any idea why my dataset is not accepted as input?
>
> Best,
>
> Robin

Looking at the XML wrapper, it expects fastqsanger ONLY. See
fastx_toolkit/fastx_quality_statistics.xml
It could in theory take fastqillumina or fastqsolexa as well, I thought
there was an open bug report on this issue but I can't find it right
now. Certainly fastx_clipper.xml was updated to use the -Q 33
switch only for Sanger quality scores, and from a quick check all
the other FASTX tools have this fix except fastx_quality_statistics.xml
Peter
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